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These data are a collection of regional GIS (Arcview shapefiles and associated Federal Geographic Data Committee (FGDC) metadata) benthic habitat files from studies conducted in specific locations within Florida. Data were collected in partnership with the NOAA Coastal Services Center following the guidelines detailed by the NOAA Coastal Change Analysis Program (C-CAP). Each regions's data is held in a separate subdirectory within this dataset. These GIS benthic data vary in type and attributes depending on the purpose of the study for each region as follows - Apalachicola Bay, sediment profiling data and benthic community information gathered from grab sampling, Dry Tortugas, RoxAnn single-beam acoustic surveys which were part of a larger biogeographic characterization effort intended to characterize benthic habitats and ocean circulation patterns in the newly established Tortugas Ecological Reserve, Florida Bay, habitat polygons developed from National Geodetic Survey aerial photography according to NOAA Coastal Change Analysis Program (C-CAP) protocol, and Indian River Lagoon, mapping SAV beds and benthic habitat according to C-CAP protocol. Each set of benthic data was developed according to protocols described in the associated FGDC metadata for each regional study. A generalized browse graphic was generated at the NODC for each region and included with these data.